Re: [COOT] Coot 0.5 and colours
FWIW: If you have an 'old' pdb file, just run it through pdbset with no keywords (other than 'END'), and the 'element column' will be added for you. Johan Paul Emsley wrote: I think Björn means that previous versions of Coot could read archaic (version 2.3) pdb files and infer the element from the atom name. Now, in 0.5 that behaviour has gone. (Yes, the element is used for colo[u]ring). There was a discussion about this (in an mmdb/CCP4 context) on CCP4-dev recently. Swings and roundabouts - or the price of progress, perhaps. Coot now reads PDB version 3.0/3.1 PDB files - we gain the ability to read modern/"proper" files from Molprobity and PHENIX but lose the ability to read archaic files (such as from (older?) versions of SOLVE/RESOLVE (I'm just guessing from what I have been told). To answer your question then, there is no way in 0.5 to turn back to the old behaviour. It might be possible in new versions to enable this, but currently I am against the idea. Paul. Steven Sheriff wrote: Bjorn: First I presume you mean element field (or column) rather than card. Second, at least since COOT 0.3, which is when I started using COOT, it has used the element field to colo[u]r atoms, so this is not new behavio[u]r. Steven Björn Kauppi wrote: Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? >> Can one turn back the 0.4.1 behaviour? Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? Can one turn back the 0.4.1 behaviour ? --Björn
Re: [COOT] Coot 0.5 and colours
> > To answer your question then, there is no way in 0.5 to turn > back to the > old behaviour. It might be possible in new versions to > enable this, but > currently I am against the idea. > Running the file through pdbset solves the missing element identifier problem -- not elegant, but quick and easy. Running the remediator script from the Richardson lab is a good solution too for other pdb version related issues (e.g. when 0.5 coot draws bonds between vicinal H atoms with old-style names): http://kinemage.biochem.duke.edu/software/remediator.php Another remark on colours in 0.5: redhat8 (non-pythonic) binaries on RHEL4 seem to have lost colours -- the model/fit/refine window, scripting window etc are all grey. JED
Re: [COOT] Coot 0.5 and colours
I think Björn means that previous versions of Coot could read archaic (version 2.3) pdb files and infer the element from the atom name. Now, in 0.5 that behaviour has gone. (Yes, the element is used for colo[u]ring). There was a discussion about this (in an mmdb/CCP4 context) on CCP4-dev recently. Swings and roundabouts - or the price of progress, perhaps. Coot now reads PDB version 3.0/3.1 PDB files - we gain the ability to read modern/"proper" files from Molprobity and PHENIX but lose the ability to read archaic files (such as from (older?) versions of SOLVE/RESOLVE (I'm just guessing from what I have been told). To answer your question then, there is no way in 0.5 to turn back to the old behaviour. It might be possible in new versions to enable this, but currently I am against the idea. Paul. Steven Sheriff wrote: Bjorn: First I presume you mean element field (or column) rather than card. Second, at least since COOT 0.3, which is when I started using COOT, it has used the element field to colo[u]r atoms, so this is not new behavio[u]r. Steven Björn Kauppi wrote: Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? >> Can one turn back the 0.4.1 behaviour? Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? Can one turn back the 0.4.1 behaviour ? --Björn
Re: [COOT] Coot 0.5 and colours
Bjorn: First I presume you mean element field (or column) rather than card. Second, at least since COOT 0.3, which is when I started using COOT, it has used the element field to colo[u]r atoms, so this is not new behavio[u]r. Steven Björn Kauppi wrote: Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? Can one turn back the 0.4.1 behaviour? --Björn *** This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the intended addressee(s) only. Any unauthorized review, use, disclosure or distribution is prohibited. If you have received this message in error, please advise the sender and delete the e-mail and any attachments from your files. Thank you! *** Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? Can one turn back the 0.4.1 behaviour? --Björn
[COOT] Coot 0.5 and colours
Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? Can one turn back the 0.4.1 behaviour? --Björn *** This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the intended addressee(s) only. Any unauthorized review, use, disclosure or distribution is prohibited. If you have received this message in error, please advise the sender and delete the e-mail and any attachments from your files. Thank you! *** Title: Coot 0.5 and colours Why is coot 0.5 relying on the element card at the right end of a pdb file for proper atom colouring? Can one turn back the 0.4.1 behaviour? --Björn
